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I've been using Codebase for a few months, and I really love it. It lets you have as many repos as you want linked to any project (and it's still considered 1 project), it's pretty affordable, and it's got a great UI. I'd +10 if I could.
–
Edan MaorJul 9 '10 at 7:43

Wedoist is a project manager that has
status updates, a task manager and a
comment system. It also uses game
mechanics to increase productivity and
usage.

Wedoist should be a lot more dynamic
than most other applications as most
of it is rendered in JavaScript and
Comet is used for realtime updates.
The future plan is to make the
realtime aspect more central (such as
adding a group chat).

It's simple and it is lean, and gaining traction from what I see around the interwebs. It is written and run by Nate Kohari, a name many people in especially the .Net community will recognize (Ninject comest to mind).

The authors themselves write:

AgileZen is a simple and flexible application that draws on ideas from lean manufacturing to provide a new way of thinking about project management. Rather than organizing tasks into a bunch of lists and trying to slice and dice your way through it, AgileZen lets you see and interact with your work visually.

Web based project management tool for straightforward task and time management. Works well for tracking project progress and also allows you to create reports and PDF invoices. Other features include a calendar, punch clock, contact management and file uploads. Basic accounts are free, while the premium version with all the features is a flat fee of $9.95 a month. Check it out at www.santexq.com

Been looking for some bug tracking software for ages and came across this. It's actually really nice to use and looks friendly unlike the majority of the others. Having used everything from Bugzilla to 16bugs it's a joy to use.

Also their pricing plan is based on the amount of users NOT the amount of projects like most others. We have a small team but lot's of projects so it started becoming very expensive with other tracking software.

The amount of projects are unlimited for ALL packages, even the free package which has up to 3 users!

It is an efficient resource planning, scheduling and management software which lets people to schedule resource effectively. The software has nice reporting features, time sheet management, drag & drop scheduling which adds a lot to its list of features. There is a trial period if you're wanting to see what it's like.